Manganese in PDB 8iqd: Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp

The structure of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp, PDB code: 8iqd was solved by Z.W.Shao, J.H.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	85.62 / 2.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	209.16, 42.814, 128.214, 90, 125.04, 90
R / Rfree (%)	24.1 / 28.3

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Manganese atom in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp (pdb code 8iqd). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 11 binding sites of Manganese where determined in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp, PDB code: 8iqd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn301 b:43.0 occ:1.00 OD2 A:ASP97 2.0 45.5 1.0 OD2 A:ASP99 2.1 40.0 1.0 OD2 A:ASP200 2.1 42.6 1.0 O A:HOH403 2.2 45.0 1.0 O A:HOH412 2.6 46.5 1.0 O1A A:DCP304 2.6 45.7 1.0 CG A:ASP99 2.9 33.1 1.0 CG A:ASP97 3.0 33.9 1.0 O5' A:DCP304 3.0 56.1 1.0 OD1 A:ASP99 3.1 31.4 1.0 CG A:ASP200 3.2 39.0 1.0 PA A:DCP304 3.3 51.6 1.0 MN A:MN303 3.4 43.4 1.0 OD1 A:ASP97 3.5 31.8 1.0 CB A:ASP200 3.6 38.0 1.0 O2A A:DCP304 3.9 58.7 1.0 C5' A:DCP304 4.0 52.6 1.0 OD1 A:ASP200 4.3 43.1 1.0 CB A:ASP97 4.3 31.1 1.0 CB A:ASP99 4.4 34.7 1.0 O3A A:DCP304 4.7 54.8 1.0 O2G A:DCP304 4.7 43.7 1.0 O1B A:DCP304 4.8 44.7 1.0 O A:ASP97 5.0 33.0 1.0

Manganese binding site 2 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn302 b:65.7 occ:1.00 OD1 C:ASP235 1.8 70.2 1.0 NE2 A:HIS179 2.3 46.3 1.0 O C:HOH403 2.6 44.3 1.0 O A:HOH414 2.7 41.6 1.0 CG C:ASP235 3.1 68.9 1.0 CE1 A:HIS179 3.2 45.7 1.0 CD2 A:HIS179 3.4 41.7 1.0 CA C:ASP235 3.9 80.5 1.0 OD2 C:ASP235 3.9 68.2 1.0 O A:ALA175 4.0 42.5 1.0 CB C:ASP235 4.1 73.0 1.0 C C:ASP235 4.1 77.2 1.0 N C:ASP237 4.1 76.8 1.0 ND1 A:HIS179 4.3 44.4 1.0 N C:PRO236 4.3 74.4 1.0 CD C:PRO236 4.4 76.1 1.0 CB A:ALA175 4.4 42.0 1.0 CG A:HIS179 4.4 42.5 1.0 C A:ALA175 4.5 38.6 1.0 O C:ASP235 4.5 75.3 1.0 O C:HOH401 4.5 45.0 1.0 NH1 B:ARG121 4.6 39.6 1.0 CA C:ASP237 4.6 75.3 1.0 N C:TYR238 4.7 72.0 1.0 C C:ASP237 4.9 72.7 1.0 N A:SER176 5.0 36.9 1.0

Manganese binding site 3 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn303 b:43.4 occ:1.00 O1B A:DCP304 2.0 44.7 1.0 OD1 A:ASP99 2.0 31.4 1.0 OD1 A:ASP97 2.1 31.8 1.0 O A:HOH411 2.3 32.5 1.0 O1A A:DCP304 2.3 45.7 1.0 O2G A:DCP304 2.4 43.7 1.0 CG A:ASP97 3.0 33.9 1.0 CG A:ASP99 3.2 33.1 1.0 PB A:DCP304 3.2 45.5 1.0 OD2 A:ASP97 3.3 45.5 1.0 MN A:MN301 3.4 43.0 1.0 PA A:DCP304 3.4 51.6 1.0 PG A:DCP304 3.5 42.5 1.0 NE2 A:HIS157 3.6 41.0 1.0 O3B A:DCP304 3.7 52.1 1.0 OD2 A:ASP99 3.7 40.0 1.0 O3A A:DCP304 3.7 54.8 1.0 O5' A:DCP304 3.8 56.1 1.0 C5' A:DCP304 3.9 52.6 1.0 OH A:TYR221 3.9 40.9 1.0 CD2 A:HIS157 4.2 35.1 1.0 O A:TYR98 4.3 29.0 1.0 O1G A:DCP304 4.3 48.0 1.0 CB A:ASP99 4.4 34.7 1.0 CB A:ASP97 4.4 31.1 1.0 O2B A:DCP304 4.5 48.4 1.0 C A:TYR98 4.6 33.0 1.0 CA A:ASP99 4.6 36.4 1.0 O A:HOH412 4.6 46.5 1.0 O2A A:DCP304 4.7 58.7 1.0 O3G A:DCP304 4.7 57.4 1.0 N A:ASP99 4.7 32.1 1.0 CZ A:TYR221 4.7 36.9 1.0 CE1 A:HIS157 4.8 42.6 1.0 C A:ASP97 4.8 31.3 1.0 CA A:ASP97 4.8 30.3 1.0 N A:TYR98 4.9 30.9 1.0

Manganese binding site 4 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn301 b:49.0 occ:1.00 OD2 B:ASP97 2.0 52.0 1.0 OD2 B:ASP200 2.1 40.8 1.0 OD2 B:ASP99 2.3 52.4 1.0 O2A B:DCP305 2.5 52.8 1.0 O5' B:DCP305 3.0 59.1 1.0 CG B:ASP99 3.0 43.7 1.0 CG B:ASP97 3.1 41.4 1.0 OD1 B:ASP99 3.1 44.8 1.0 CG B:ASP200 3.2 43.5 1.0 PA B:DCP305 3.2 53.8 1.0 MN B:MN303 3.4 53.6 1.0 OD1 B:ASP97 3.5 41.3 1.0 CB B:ASP200 3.7 44.3 1.0 C5' B:DCP305 3.9 57.4 1.0 O1A B:DCP305 3.9 63.7 1.0 OD1 B:ASP200 4.3 49.2 1.0 CB B:ASP97 4.3 40.0 1.0 CB B:ASP99 4.5 45.6 1.0 O3A B:DCP305 4.6 57.2 1.0 O3G B:DCP305 4.6 56.0 1.0 O2B B:DCP305 4.6 50.5 1.0 O B:ASP97 4.9 39.9 1.0

Manganese binding site 5 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn302 b:61.4 occ:1.00 OD1 D:ASP235 2.0 66.2 1.0 NE2 B:HIS179 2.3 45.9 1.0 O A:HOH413 2.6 45.6 1.0 CE1 B:HIS179 3.2 44.6 1.0 CG D:ASP235 3.3 65.9 1.0 CD2 B:HIS179 3.4 40.1 1.0 CB D:ASP237 3.9 68.6 1.0 OD2 D:ASP235 4.0 65.7 1.0 O B:ALA175 4.0 39.3 1.0 N D:ASP237 4.1 73.0 1.0 CA D:ASP235 4.1 76.9 1.0 C D:ASP235 4.2 78.4 1.0 CB D:ASP235 4.3 69.9 1.0 O A:HOH408 4.3 51.4 1.0 CB B:ALA175 4.4 49.3 1.0 ND1 B:HIS179 4.4 40.9 1.0 N D:TYR238 4.4 66.5 1.0 CA D:ASP237 4.4 72.0 1.0 CG B:HIS179 4.5 41.0 1.0 C B:ALA175 4.5 40.2 1.0 NH1 A:ARG121 4.5 32.0 1.0 N D:PRO236 4.5 75.4 1.0 CD D:PRO236 4.5 73.8 1.0 O D:ASP235 4.6 80.3 1.0 C D:ASP237 4.7 68.5 1.0 CB D:TYR238 4.8 57.1 1.0 CA B:ALA175 5.0 41.2 1.0

Manganese binding site 6 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn303 b:53.6 occ:1.00 O2B B:DCP305 1.9 50.5 1.0 OD1 B:ASP99 2.1 44.8 1.0 OD1 B:ASP97 2.1 41.3 1.0 O3G B:DCP305 2.2 56.0 1.0 O B:HOH404 2.3 39.3 1.0 O2A B:DCP305 2.4 52.8 1.0 CG B:ASP97 3.0 41.4 1.0 PB B:DCP305 3.0 54.0 1.0 CG B:ASP99 3.3 43.7 1.0 OD2 B:ASP97 3.3 52.0 1.0 PG B:DCP305 3.3 54.0 1.0 MN B:MN301 3.4 49.0 1.0 PA B:DCP305 3.4 53.8 1.0 O3B B:DCP305 3.5 63.4 1.0 O3A B:DCP305 3.6 57.2 1.0 NE2 B:HIS157 3.7 44.4 1.0 OH B:TYR221 3.8 43.5 1.0 OD2 B:ASP99 3.8 52.4 1.0 O5' B:DCP305 3.9 59.1 1.0 C5' B:DCP305 4.0 57.4 1.0 O2G B:DCP305 4.1 52.8 1.0 CD2 B:HIS157 4.3 39.5 1.0 O B:TYR98 4.3 39.4 1.0 O1B B:DCP305 4.3 58.1 1.0 CB B:ASP97 4.4 40.0 1.0 CB B:ASP99 4.4 45.6 1.0 O1G B:DCP305 4.5 70.3 1.0 C B:TYR98 4.6 39.6 1.0 CA B:ASP99 4.6 43.0 1.0 CZ B:TYR221 4.7 41.5 1.0 N B:ASP99 4.7 40.0 1.0 C B:ASP97 4.8 39.1 1.0 O1A B:DCP305 4.8 63.7 1.0 CE1 B:HIS157 4.8 42.1 1.0 CA B:ASP97 4.8 35.9 1.0 N B:TYR98 4.9 36.8 1.0

Manganese binding site 7 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range:

Manganese binding site 8 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn301 b:77.5 occ:1.00 OD2 C:ASP200 1.8 71.2 1.0 OD2 C:ASP97 1.9 64.6 1.0 OD2 C:ASP99 2.5 62.9 1.0 CG C:ASP200 2.9 66.0 1.0 CG C:ASP97 3.0 61.8 1.0 CG C:ASP99 3.4 69.9 1.0 CB C:ASP200 3.4 66.3 1.0 OD1 C:ASP99 3.4 69.9 1.0 OD1 C:ASP97 3.5 65.2 1.0 MN C:MN302 3.5 67.6 1.0 O3G C:DCP303 3.7 67.2 1.0 OD1 C:ASP200 4.0 66.1 1.0 CB C:ASP97 4.2 61.0 1.0 O1G C:DCP303 4.6 63.8 1.0 CA C:ASP200 4.8 62.4 1.0 CB C:ASP99 4.8 61.4 1.0 O1B C:DCP303 4.8 70.7 1.0 PG C:DCP303 4.8 66.8 1.0 O C:ASP97 4.9 60.9 1.0

Manganese binding site 9 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn302 b:67.6 occ:1.00 OD1 C:ASP97 1.9 65.2 1.0 O1B C:DCP303 2.0 70.7 1.0 OD1 C:ASP99 2.3 69.9 1.0 O1G C:DCP303 2.4 63.8 1.0 CG C:ASP97 2.8 61.8 1.0 O3G C:DCP303 3.0 67.2 1.0 OD2 C:ASP97 3.0 64.6 1.0 PG C:DCP303 3.0 66.8 1.0 PB C:DCP303 3.1 62.5 1.0 O3B C:DCP303 3.4 53.6 1.0 NE2 C:HIS157 3.4 58.2 1.0 CG C:ASP99 3.5 69.9 1.0 MN C:MN301 3.5 77.5 1.0 O3A C:DCP303 3.9 70.0 1.0 OH C:TYR221 3.9 54.8 1.0 OD2 C:ASP99 3.9 62.9 1.0 CD2 C:HIS157 4.0 57.3 1.0 CB C:ASP97 4.1 61.0 1.0 O2B C:DCP303 4.3 58.3 1.0 O C:TYR98 4.4 61.2 1.0 O2G C:DCP303 4.5 54.5 1.0 CE1 C:HIS157 4.6 61.5 1.0 CA C:ASP97 4.6 59.6 1.0 C C:ASP97 4.7 57.2 1.0 C C:TYR98 4.7 60.5 1.0 CZ C:TYR221 4.7 55.2 1.0 CB C:ASP99 4.7 61.4 1.0 N C:TYR98 4.8 57.4 1.0 N C:ASP99 4.9 62.3 1.0 CA C:ASP99 4.9 60.0 1.0 CE2 C:TYR221 4.9 53.3 1.0

Manganese binding site 10 out of 11 in the Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Crystal Structure of Asfvprimpol N-Terminal Prim/Pol Domain in Complex with MN2+ and Dctp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn301 b:83.8 occ:1.00 O3G D:DCP303 2.0 84.9 1.0 OD2 D:ASP200 2.1 74.6 1.0 OD2 D:ASP97 2.1 77.7 1.0 OD2 D:ASP99 2.4 78.4 1.0 CG D:ASP200 2.9 74.9 1.0 CG D:ASP97 3.0 72.7 1.0 CG D:ASP99 3.2 73.2 1.0 CB D:ASP200 3.2 76.0 1.0 OD1 D:ASP99 3.3 74.7 1.0 PG D:DCP303 3.3 91.9 1.0 OD1 D:ASP97 3.6 70.8 1.0 MN D:MN302 3.6 76.1 1.0 O2G D:DCP303 3.7 82.0 1.0 OD1 D:ASP200 4.0 75.3 1.0 CB D:ASP97 4.0 66.9 1.0 O1G D:DCP303 4.2 97.0 1.0 O3B D:DCP303 4.4 80.0 1.0 CA D:ASP200 4.6 74.5 1.0 O D:ASP97 4.6 69.7 1.0 CB D:ASP99 4.6 69.4 1.0 O2B D:DCP303 4.9 77.7 1.0 O2A D:DCP303 4.9 79.4 1.0

Z.W.Shao, J.H.Gan. Structures and Implications of the Primpol Protein of African Swine Fever Virus To Be Published.